Peakon solutions of the shallow water equation. - Mark S. Alber; Charles Miller (Appl. Math. Lett., 2001)

On Cellular Automaton Approaches to Modeling Biological Cells. - Mark S. Alber; Maria A. Kiskowski; James A. Glazier; Yi Jiang (Mathematical Systems Theory in Biology, Communications, Computation, and Finance, 2003)

Multi-model Simulations of Chicken Limb Morphogenesis. - Rajiv Chaturvedi; Jesús A. Izaguirre; Chengbang Huang; Trevor M. Cickovski; P. Virtue; Gilberto L. Thomas; Gabor Forgacs; Mark S. Alber; H. George E. Hentschel; Stuart A. Newman; James A. Glazier (International Conference on Computational Science, 2003)

A Cellular Automata Model of Early T Cell Recognition. - Arancha Casal; Cenk Sumen; Tim Reddy; Mark S. Alber; Peter P. Lee (ACRI, 2004)

A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb. - Rajiv Chaturvedi; Chengbang Huang; Jesús A. Izaguirre; Stuart A. Newman; James A. Glazier; Mark S. Alber (ACRI, 2004)

COMPUCELL, a multi-model framework for simulation of morphogenesis. - Jesús A. Izaguirre; Rajiv Chaturvedi; Chengbang Huang; Trevor M. Cickovski; J. Coffland; Gilberto L. Thomas; Gabor Forgacs; Mark S. Alber; H. George E. Hentschel; Stuart A. Newman; James A. Glazier (Bioinform., 2004)

Special Issue on Multiscale Modeling in Biology. - Mark S. Alber; Thomas Yizhao Hou; James A. Glazier; Yi Jiang (Multiscale Model. Simul., 2005)

A Framework for Three-Dimensional Simulation of Morphogenesis. - Trevor M. Cickovski; Chengbang Huang; Rajiv Chaturvedi; Tilmann Glimm; H. George E. Hentschel; Mark S. Alber; James A. Glazier; Stuart A. Newman; Jesús A. Izaguirre (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis. - Nan Chen; James A. Glazier; Mark S. Alber (ACRI, 2006)

CA Models of Myxobacteria Swarming. - Yilin Wu 004; Nan Chen; Matthew Rissler; Yi Jiang; Dale Kaiser; Mark S. Alber (ACRI, 2006)

On Modeling Complex Collective Behavior in Myxobacteria. - Yi Jiang; Olga Sozinova; Mark S. Alber (Adv. Complex Syst., 2006)

Multiscale Agent-based Simulation for Chondrogenic Pattern Formation in Vitro. - Scott Christley; Xuelian Zhu; Stuart A. Newman; Mark S. Alber (Cybern. Syst., 2007)

A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis. - Nan Chen; James A. Glazier; Jesús A. Izaguirre; Mark S. Alber (Comput. Phys. Commun., 2007)

From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. - Trevor M. Cickovski; Kedar Aras; Maciej Swat; Roeland Merks; Tilmann Glimm; H. George E. Hentschel; Mark S. Alber; James A. Glazier; Stuart A. Newman; Jesús A. Izaguirre (Comput. Sci. Eng., 2007)

Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model. - Scott Christley; Mark S. Alber; Stuart A. Newman (PLoS Comput. Biol., 2007)

Social Interactions in Myxobacterial Swarming. - Yilin Wu 004; Yi Jiang; Dale Kaiser; Mark S. Alber (PLoS Comput. Biol., 2007)

Segmentation, reconstruction, and analysis of blood thrombi in 2-photon microscopy images. - Jian Mu; Xiaomin Liu; Malgorzata M. Kamocka; Zhiliang Xu; Mark S. Alber; Elliot D. Rosen; Danny Z. Chen (CBMS, 2009)

Existence of global solutions of a macroscopic model of cellular motion in a chemotactic field. - Mark S. Alber; Richard Gejji; Bogdan Kazmierczak (Appl. Math. Lett., 2009)

Application of Discontinuous Galerkin Methods for Reaction-Diffusion Systems in Developmental Biology. - Jianfeng Zhu; Yong-Tao Zhang; Stuart A. Newman; Mark S. Alber (J. Sci. Comput., 2009)

Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus Xanthus. - Faruck Morcos; Marcin Sikora; Mark S. Alber; Dale Kaiser; Jesús A. Izaguirre (Pacific Symposium on Biocomputing, 2010)

Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images. - Jian Mu; Xiaomin Liu; Malgorzata M. Kamocka; Zhiliang Xu; Mark S. Alber; Elliot D. Rosen; Danny Z. Chen (EURASIP J. Adv. Signal Process., 2010)

Belief propagation estimation of protein and domain interactions using the sum-product algorithm. - Faruck Morcos; Marcin Sikora; Mark S. Alber; Dale Kaiser; Jesús A. Izaguirre (IEEE Trans. Inf. Theory, 2010)

Identification and classification of cells in multispectral microscopy images of lymph nodes. - Xiaomin Liu; Alvernia F. Setiadi; Mark S. Alber; Peter P. Lee; Danny Z. Chen (Image Processing, 2011)

Detecting and Tracking Motion of Myxococcus xanthus Bacteria in Swarms. - Xiaomin Liu; Cameron W. Harvey; Haitao Wang 001; Mark S. Alber; Danny Z. Chen (MICCAI (1), 2012)

Automatic segmentation and analysis of fibrin networks in 3D confocal microscopy images. - Xiaomin Liu; Jian Mu; Kellie R. Machlus; Alisa S. Wolberg; Elliot D. Rosen; Zhiliang Xu; Mark S. Alber; Danny Z. Chen (Image Processing, 2012)

Interconnected Cavernous Structure of Bacterial Fruiting Bodies. - Cameron W. Harvey; Huijing Du; Zhiliang Xu; Dale Kaiser; Igor S. Aranson; Mark S. Alber (PLoS Comput. Biol., 2012)

Fibrin Networks Regulate Protein Transport during Thrombus Development. - Oleg V. Kim; Zhiliang Xu; Elliot D. Rosen; Mark S. Alber (PLoS Comput. Biol., 2013)

An Automated Approach for Fibrin Network Segmentation and Structure Identification in 3D Confocal Microscopy Images. - Jianxu Chen 001; Oleg V. Kim; Rustem I. Litvinov; John W. Weisel; Mark S. Alber; Danny Ziyi Chen (CBMS, 2014)

A Matching Model Based on Earth Mover's Distance for Tracking Myxococcus Xanthus. - Jianxu Chen 001; Cameron W. Harvey; Mark S. Alber; Danny Ziyi Chen (MICCAI (2), 2014)

A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms. - Jianxu Chen 001; Shant Mahserejian; Mark S. Alber; Danny Z. Chen (MICCAI (3), 2015)

Segmentation and tracking of Pseudomonas aeruginosa for cell dynamics analysis in time-lapse images. - Jianxu Chen 001; Yiqing Cai; Chen Wei; Lin Yang 003; Mark S. Alber; Danny Ziyi Chen (ISBI, 2016)

Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation. - Jianxu Chen 001; Lin Yang 003; Yizhe Zhang 001; Mark S. Alber; Danny Ziyi Chen (NIPS, 2016)

A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms. - Jianxu Chen 001; Mark S. Alber; Danny Ziyi Chen (IEEE Trans. Medical Imaging, 2016)

Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia. - Ali Nematbakhsh; Wenzhao Sun; Pavel A. Brodskiy; Aboutaleb Amiri; Cody Narciso; Zhiliang Xu; Jeremiah J. Zartman; Mark S. Alber (PLoS Comput. Biol., 2017)

Integrating machine learning and multiscale modeling - perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences. - Mark S. Alber; Adrian Buganza Tepole; William R. Cannon; Suvranu De; Salvador Dura-Bernal; Krishna C. Garikipati; George E. Karniadakis; William W. Lytton; Paris Perdikaris; Linda R. Petzold; Ellen Kuhl (npj Digit. Medicine, 2019)

Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix. - Ali Nematbakhsh; Megan Levis; Nilay Kumar; Weitao Chen; Jeremiah J. Zartman; Mark S. Alber (PLoS Comput. Biol., 2020)

Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease. - Noelia Grande Gutiérrez; Mark S. Alber; Andrew M. Kahn; Jane C. Burns; Mathew Mathew; Brian W. McCrindle; Alison L. Marsden (PLoS Comput. Biol., 2021)

Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance. - Mikahl Banwarth-Kuhn; Kevin Rodriguez; Christian Michael; Calvin-Khang Ta; Alexander Plong; Eric Bourgain-Chang; Ali Nematbakhsh; Weitao Chen; Amit K. Roy-Chowdhury; G. Venugopala Reddy; Mark S. Alber (PLoS Comput. Biol., 2022)

Learning Deformable 3D Graph Similarity to Track Plant Cells in Unregistered Time Lapse Images. - Md Shazid Islam; Arindam Dutta; Calvin-Khang Ta; Kevin Rodriguez; Christian Michael; Mark S. Alber; G. Venugopala Reddy; Amit K. Roy-Chowdhury (CoRR, 2023)

Study of impacts of two types of cellular aging on the yeast bud morphogenesis. - Kevin Tsai; Zhen Zhou; Jiadong Yang; Zhiliang Xu; Shixin Xu; Roya Zandi; Nan Hao; Weitao Chen; Mark S. Alber (PLoS Comput. Biol., 2024)